On 12/12/2010 6:25 PM, leila separdar wrote:
yes I have read them many times
OK, so you know how to understand how your .top files are describing the nonbonded interactions between your atom types. Now you just need to combine the two. Probably you want one atomtypes section, etc. If you want them to interact, then you'll need to define parameters accordingly, either using combination rules (see manual) or with explicit nonbond_params (see manual).
Mark
On Sun, Dec 12, 2010 at 10:41 AM, Mark Abraham <[email protected] <mailto:[email protected]>> wrote:On 12/12/2010 6:08 PM, leila separdar wrote: I want to simulate a binary lenard jones system. I have .top and .gro file for both A and B atom types . how can I mix this two atom types ? do I must regard the lenard jones potential between this two atom type or not? and where I must put C12 and C6 parameters for interaction between these two atoms? Have you done the necessary background reading in chapters 4 and 4 of the manual? Mark-- gmx-users mailing list [email protected]<mailto:[email protected]> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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